annotate macros.xml @ 11:5a326a6fa105 draft default tip

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
author artbio
date Fri, 17 Oct 2025 17:21:17 +0000
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5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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1 <macros>
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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2 <token name="@TOOL_VERSION@">0.2.8</token>
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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3 <token name="@GALAXY_VERSION@">4</token>
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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4
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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5 <!-- Requirements for lumpy_smoove (Python 2.7 environment) -->
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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6 <xml name="lumpy_smoove_requirements">
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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7 <requirements>
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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8 <requirement type="package" version="0.2.8">smoove</requirement>
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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9 <requirement type="package" version="0.7.1">svtyper</requirement>
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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10 <requirement type="package" version="2.7">python</requirement>
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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11 </requirements>
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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12 </xml>
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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14 <!-- Requirements for vcf2hrdetect (Python 3.9 environment) -->
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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15 <xml name="vcf2hrdetect_requirements">
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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16 <requirements>
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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17 <requirement type="package" version="3.9">python</requirement>
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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18 </requirements>
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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19 </xml>
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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21 <xml name="stdio">
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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22 <stdio>
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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23 <exit_code range="1:" level="fatal" description="Tool exception" />
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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24 </stdio>
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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25 </xml>
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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26 <token name="@pipefail@"><![CDATA[set -o | grep -q pipefail && set -o pipefail;]]></token>
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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27 <token name="@set_fasta_index@"><![CDATA[
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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28 #if str( $reference_source.reference_source_selector ) == "history":
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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29 ln -s '${reference_source.ref_file}' reference.fa &&
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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30 samtools faidx 'reference.fa' 2>&1 || echo "Error running samtools faidx for lumpy_smoove" >&2 &&
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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31 #else:
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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32 ln -s '${reference_source.index.fields.path}' reference.fa &&
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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33 ln -s '${reference_source.index.fields.path}.fai' reference.fa.fai &&
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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34 #end if
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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35 ]]></token>
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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36 <macro name="reference_source_conditional">
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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37 <conditional name="reference_source">
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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38 <param name="reference_source_selector" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options.">
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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39 <option value="cached">Use a built-in genome index</option>
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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40 <option value="history">Use a genome from history and build index</option>
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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41 </param>
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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42 <when value="cached">
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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43 <param name="index" type="select" label="Using built-in genome" help="Select genome from the list">
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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44 <options from_data_table="fasta_indexes">
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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45 <filter type="sort_by" column="2" />
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46 <validator type="no_options" message="No indexes are available" />
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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47 </options>
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48 </param>
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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49 </when>
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50 <when value="history">
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51 <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" />
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52 </when>
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53 </conditional>
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54 </macro>
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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55 </macros>
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56
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